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Liang H, Qi H, Wang C, Wang Y, Liu M, Chen J, Sun X, Xia T, Feng S, Chen C, Zheng D. Analysis of the complete mitogenomes of three high economic value tea plants (Tea-oil Camellia) provide insights into evolution and phylogeny relationship. FRONTIERS IN PLANT SCIENCE 2025; 16:1549185. [PMID: 40343121 PMCID: PMC12058841 DOI: 10.3389/fpls.2025.1549185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2024] [Accepted: 03/18/2025] [Indexed: 05/11/2025]
Abstract
Introduction Tea-oil Camellia species play a crucial economic and ecological role worldwide, yet their mitochondrial genomes remain largely unexplored. Methods In this study, we assembled and analyzed the complete mitochondrial genomes of Camellia oleifera and C. meiocarpa, revealing multi-branch structures that deviate from the typical circular mitochondrial genome observed in most plants. The assembled mitogenomes span 953,690 bp (C. oleifera) and 923,117 bp (C. meiocarpa), containing 74 and 76 annotated mitochondrial genes, respectively. Results Comparative genomic analyses indicated that C. oleifera and C. meiocarpa share a closer genetic relationship, whereas C. drupifera is more distantly related. Codon usage analysis revealed that natural selection plays a dominant role in shaping codon bias in these mitochondrial genomes. Additionally, extensive gene transfer events were detected among the three species, highlighting the dynamic nature of mitochondrial genome evolution in Tea-oil Camellia. Phylogenetic reconstruction based on mitochondrial genes exhibited incongruence with chloroplast phylogenies, suggesting potential discordance due to hybridization events, incomplete lineage sorting (ILS), or horizontal gene transfer (HGT). Furthermore, we identified species-specific mitochondrial markers, which provide valuable molecular tools for distinguishing Tea-oil Camellia species. Discussion Our findings enhance the understanding of mitochondrial genome evolution and genetic diversity in Tea-oil Camellia, offering essential genomic resources for phylogenetics, species identification, and evolutionary research in woody plants.
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Affiliation(s)
- Heng Liang
- Institute of Tropical Horticulture Research, Hainan Academy of Agricultural Sciences, Haikou, China
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, China
- Key Laboratory of Tropic Special Economic Plant Innovation and Utilization, Haikou, China
- Key Laboratory of Tropic Special Economic Plant Innovation and Utilization, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Huasha Qi
- Institute of Tropical Horticulture Research, Hainan Academy of Agricultural Sciences, Haikou, China
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, China
- Key Laboratory of Tropic Special Economic Plant Innovation and Utilization, Haikou, China
- Key Laboratory of Tropic Special Economic Plant Innovation and Utilization, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Chunmei Wang
- Institute of Tropical Horticulture Research, Hainan Academy of Agricultural Sciences, Haikou, China
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, China
- Key Laboratory of Tropic Special Economic Plant Innovation and Utilization, Haikou, China
- Key Laboratory of Tropic Special Economic Plant Innovation and Utilization, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Yidan Wang
- School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Moyang Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiali Chen
- Institute of Tropical Horticulture Research, Hainan Academy of Agricultural Sciences, Haikou, China
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, China
- Key Laboratory of Tropic Special Economic Plant Innovation and Utilization, Haikou, China
- Key Laboratory of Tropic Special Economic Plant Innovation and Utilization, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Xiuxiu Sun
- Institute of Tropical Horticulture Research, Hainan Academy of Agricultural Sciences, Haikou, China
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, China
- Key Laboratory of Tropic Special Economic Plant Innovation and Utilization, Haikou, China
- Key Laboratory of Tropic Special Economic Plant Innovation and Utilization, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Tengfei Xia
- Institute of Tropical Horticulture Research, Hainan Academy of Agricultural Sciences, Haikou, China
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, China
- Key Laboratory of Tropic Special Economic Plant Innovation and Utilization, Haikou, China
- Key Laboratory of Tropic Special Economic Plant Innovation and Utilization, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Shiling Feng
- College of Life Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Cheng Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Daojun Zheng
- Institute of Tropical Horticulture Research, Hainan Academy of Agricultural Sciences, Haikou, China
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, China
- Key Laboratory of Tropic Special Economic Plant Innovation and Utilization, Haikou, China
- Key Laboratory of Tropic Special Economic Plant Innovation and Utilization, Hainan Academy of Agricultural Sciences, Haikou, China
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Yang H, Ni Y, Li J, Chen H, Liu C. Unveiling the mitochondrial genome of Salvia splendens insights into the evolutionary traits within the genus Salvia. Sci Rep 2025; 15:13344. [PMID: 40246928 PMCID: PMC12006378 DOI: 10.1038/s41598-025-96637-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 03/31/2025] [Indexed: 04/19/2025] Open
Abstract
Previously, we resolved the complete sequences of the mitochondrial genomes (mitogenome) of two Salvia species (S. miltiorrhiza and S. officinalis). The major configurations of these two species were two circular chromosomes. In this study, we further studied the mitogenome of a floral species of Salvia (Salvia splendens) to understand the diversity and evolution of the Salvia mitogenomes. We sequenced the total DNAs of S. splendens using the Nanopore and Illumina platforms and assembled the mitogenome using a hybrid assembly strategy. The major configurations of the S. splendens were two circular chromosomes with lengths of 182,239 and 165,055 bp. There were 32 protein-coding genes (PCGs), three rRNA genes, and 18 tRNA genes annotated in the S. splendens mitogenome. We found 56 pairs of repetitive sequences in the S. splendens mitogenome. Three of them (R01, 04, and 07) could mediate recombination, whose products could be identified by the mapping of Nanopore reads, PCR amplifications, and Sanger sequencing of the PCR products. 457 RNA editing sites were identified in the S. splendens mitochondrial RNAs when comparing the RNA-seq data with their corresponding DNA templates. We showed that S. splendens was a sister taxon to S. miltiorrhiza based on the mitogenomes, consistent with the phylogeny determined with the plastome sequences. Crucially, we developed 12 mitochondrial markers sourced from mitochondrial intron regions to facilitate the identification of three Salvia species. Our study offers a comprehensive view of the structure of the Salvia mitogenomes and provides robust mitochondrial markers for Salvia species identification.
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Affiliation(s)
- Heyu Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Yang Ni
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Jingling Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Haimei Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China.
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China.
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Liang H, Deng J, Wang Y, Gao G, Yang R. The first complete mitochondrial genome of Curcuma amarissima (Zingiberaceae): insights into multi-branch structure, codon usage, and phylogenetic evolution. BMC Genomics 2025; 26:343. [PMID: 40188039 PMCID: PMC11971759 DOI: 10.1186/s12864-025-11540-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Accepted: 03/27/2025] [Indexed: 04/07/2025] Open
Abstract
BACKGROUND As a key genus in Zingiberaceae, Curcuma is widely studied for its taxonomic diversity, the presence of bioactive curcuminoids and volatile oils, and its extensive applications in traditional medicine and economic products such as spices and cosmetics. Although chloroplast genomes have been assembled and published for over 20 Curcuma species, mitochondrial genomic data remain limited. RESULTS We successfully sequenced, assembled, and annotated the mitogenome of Curcuma amarissima (C. amarissima) using both Illumina short reads and Nanopore long reads, achieving the first complete mitogenome characterization in the Zingiberaceae family. The C. amarissima mitogenome features a unique multi-branched structure, spanning 6,505,655 bp and consisting of 39 distinct segments. It contains a total of 43 protein-coding genes, 63 tRNA genes, and 4 rRNA genes, with a GC content of 44.04%. Codon usage analysis indicated a weak bias, with neutrality plot analysis suggesting natural selection as a key factor shaping mitochondrial codon usage in C. amarissima. The mitogenome provides valuable insights into genome size, coding genes, structural features, RNA editing, repetitive sequences, and sequence migration, enhancing our understanding of the evolution and molecular biology of multi-branched mitochondria in Zingiberaceae. The high frequency of repeat sequences may contribute to the structural stability of the mitochondria. Comparing chloroplast genome, phylogenetic analysis based on the mitochondrial genome establishes a foundation for further exploration of evolutionary relationships within Zingiberaceae. CONCLUSIONS In short, the mitochondrial genome characterized here advances our understanding of multi-branched mitogenome organization in Zingiberaceae and offers useful genomic resources that may support future breeding, germplasm conservation, and phylogenetic studies, though further research is necessary.
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Affiliation(s)
- Heng Liang
- Institute of Tropical Horticulture Research, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan Province, 625014, China
| | - Jiabin Deng
- College of Chuanjiu, Sichuan Vocational College of Chemical Technology, Luzhou, 646300, China
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan Province, 625014, China
| | - Yidan Wang
- School of Life Sciences, Technical University of Munich, Freising, 85354, Germany
| | - Gang Gao
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China.
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan Province, 625014, China.
| | - Ruiwu Yang
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan Province, 625014, China
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Ma Y, López-Pujol J, Yan D, Deng Z, Zhou Z, Niu J. Complete mitochondrial genomes of the hemiparasitic genus Cymbaria (Orobanchaceae): insights into repeat-mediated recombination, phylogenetic relationships, and horizontal gene transfer. BMC Genomics 2025; 26:314. [PMID: 40165089 PMCID: PMC11956449 DOI: 10.1186/s12864-025-11474-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Accepted: 03/12/2025] [Indexed: 04/02/2025] Open
Abstract
BACKGROUND The Orobanchaceae family is widely recognized as an exemplary model system for examining the evolutionary dynamics of parasitic plants. However, reports on the mitochondrial genome (mitogenome) of the hemiparasitic tribe Cymbarieae are currently lacking. Here, we sequenced, assembled and characterized the complete mitogenome of the genus Cymbaria L. sensu stricto (C. mongolica and C. daurica). RESULTS A total of 51 unique mitochondrial genes, including 33 protein-coding genes, three rRNA genes, and 15 tRNA genes, are shared by the mitogenomes of the two hemiparasitic plants, exhibiting the gene content characteristic of autotrophic plants. The mitogenomes of C. mongolica and C. daurica are characterized by a pentacyclic chromosome structure (their major conformation), with lengths of 1,576,465 bp and 1,539,836 bp, respectively. Moreover, we identified and validated the presence of four minor conformations mediated by four pairs of large repeats (> 1000 bp in size) in C. mongolica and eight minor conformations mediated by six large repeats in C. daurica. We further explored codon usage, RNA editing sites, selective pressure, and nucleotide diversity in two Cymbaria mitogenomes. Phylogenetic analyses of 26 species of Lamiales revealed that the two Cymbaria species form a sister clade to the other lineages of Orobanchaceae. Extensive mitogenomic rearrangements are also observed between Cymbaria and five closely related species. Although we identified mitochondrial plastid sequences in the Cymbaria mitogenomes, The mitochondrial plastid sequences (MTPTs) in their mitogenomes represent only 2.37% and 1.74%, respectively. Additionally, there is minimal evidence of intracellular and horizontal gene transfer, with only a few genes (rpl22, rps3, and ycf2) showing low bootstrap support (BS ≤ 70%) for the relationships with the potential host plants Allium mongolicum, Leymus chinensis, and Saposhnikovia divaricata, respectively. CONCLUSIONS We reported the mitochondrial genome in hemiparasitic Cymbaria species for the first time, which are characterized by multiple repeat-mediated recombination and little to no intracellular and horizontal gene transfer. Our findings provide valuable genetic insights for further studies on the mitogenome evolution of hemiparasitic plants.
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Affiliation(s)
- Yang Ma
- School of Ecology and Environment, Inner Mongolia University, Hohhot, 010020, People's Republic of China
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB), CSIC-CMCNB, Barcelona, 08038, Spain
- Escuela de Ciencias Ambientales, Universidad Espíritu Santo (UEES), Samborondón, 091650, Ecuador
| | - Dongqing Yan
- School of Ecology and Environment, Inner Mongolia University, Hohhot, 010020, People's Republic of China
| | - Zekun Deng
- School of Ecology and Environment, Inner Mongolia University, Hohhot, 010020, People's Republic of China
| | - Zhen Zhou
- School of Ecology and Environment, Inner Mongolia University, Hohhot, 010020, People's Republic of China
| | - Jianming Niu
- School of Ecology and Environment, Inner Mongolia University, Hohhot, 010020, People's Republic of China.
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Hohhot, 010020, People's Republic of China.
- Inner Mongolia Key Laboratory of Grassland Ecology and the Candidate State Key Laboratory of Ministry of Science and Technology, Hohhot, 010020, People's Republic of China.
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Gong Y, Qin Y, Liu R, Wei Y, Liu H, Li P, Zhou G. Assembly and comparative analysis of the complete mitochondrial genome of Lactuca sativa var. ramosa Hort. Sci Rep 2025; 15:9257. [PMID: 40102506 PMCID: PMC11920196 DOI: 10.1038/s41598-025-93762-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Accepted: 03/10/2025] [Indexed: 03/20/2025] Open
Abstract
Lettuce (Lactuca sativa var. ramosa Hort) is an important leaf vegetable that widely cultivates due to its high-quality, short growth cycle, and less diseases. L. sativa var. ramosa Hort belongs to Asteraceae family and its evolutionary relationships with related species of Asteraceae are not completely assessed based on genome sequences. Here, we assembled the whole mitochondrial (mt) genome of L. sativa var. ramosa Hort, and performed a comparative with other related species. The L. sativa var. ramosa Hort mt genome has a typical circular structure with a length of 363,324 bp, within GC content accounted for 45.35%. In total of 71 genes, comprising 35 protein-coding genes (PCGs), 6 rRNAs, 28 tRNAs, and 2 pseudogenes were annotated. Codon preference, RNA-editing sites, repetitive sequences, and genes migrating from chloroplast (cp) to mt genomes were investigated in the L. sativa var. ramosa Hort mt genome. Nucleotide diversity (Pi) showed that the L. sativa var. ramosa Hort mt genome was relatively conserved. A Bayesian phylogenetic tree showed that L. sativa var. ramosa Hort was closely to L. sativa var. capitata and L. virosa, which belonged to the Lactuca genus in the Asteraceae family. Our findings will provide useful information to explore genetic variation, genetic diversity, and molecular breeding on the Lactuca genus.
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Affiliation(s)
- Yihui Gong
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi, 417000, China.
| | - Yalin Qin
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Rong Liu
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Yuanyuan Wei
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Haotian Liu
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Peng Li
- Xiangtan Agricultural Science Research Institute, Xiangtan, 411100, China
| | - Guihua Zhou
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi, 417000, China.
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Liu J, Yu S, Lü P, Gong X, Sun M, Tang M. De novo assembly and characterization of the complete mitochondrial genome of Phellodendron amurense reveals three repeat-mediated recombination. Gene 2025; 935:149031. [PMID: 39461576 DOI: 10.1016/j.gene.2024.149031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 10/18/2024] [Accepted: 10/21/2024] [Indexed: 10/29/2024]
Abstract
Phellodendron amurense Rupr., a rare herb renowned for its medicinal and ecological significance, has remained genetically unexplored at the mitochondrial level until now. This study presents the first-ever systematic assembly and annotation of the complete mitochondrial genome of P. amurense, achieved through a hybrid strategy combining Illumina and Nanopore sequencing data. The mitochondrial genome spans 566,285 bp with a GC content of 45.51 %, structured into two circular molecules. Our comprehensive analysis identified 32 protein-coding genes (PCGs), 33 tRNA genes, and 3 rRNA genes, alongside 181 simple sequence repeats, 19 tandem repeats, and 310 dispersed repeats. Notably, multiple genome conformations were predicted due to repeat-mediated homologous recombination. Additionally, we assembled the chloroplast genome, identifying 21 mitochondrial plastid sequences that provide insights into organelle genome interactions. A total of 380 RNA-editing sites within the mitochondrial PCGs were predicted, enhancing our understanding of gene regulation and function. Phylogenetic analysis using mitochondrial PCGs from 30 species revealed evolutionary relationships, confirming the homology between P. amurense and Citrus species. This foundational study offers a valuable genetic resource for the Rutaceae family, facilitating further research into genetic evolution and molecular diversity in plant mitochondrial genomes.
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Affiliation(s)
- Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Shaoshuai Yu
- Department of Pharmacy, Affiliated People's Hospital of Jiangsu University, Zhenjiang 212001, Jiangsu, China
| | - Peng Lü
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Xun Gong
- Department of Rheumatology & Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, Jiangsu, China
| | - Mengmeng Sun
- Changchun University of Chinese Medicine, Changchun 130117, Jilin, China
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
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Zhang H, Yan M, Li L, Jiang Z, Xiong Y, Wang Y, Akogwu CO, Tolulope OM, Zhou H, Sun Y, Wang H. Assembly and comparative analysis of the complete mitochondrial genome of red raspberry (Rubus idaeus L.) revealing repeat-mediated recombination and gene transfer. BMC PLANT BIOLOGY 2025; 25:85. [PMID: 39838290 PMCID: PMC11752677 DOI: 10.1186/s12870-024-05969-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Accepted: 12/13/2024] [Indexed: 01/23/2025]
Abstract
BACKGROUND Red raspberry (Rubus idaeus L.) is a renowned fruit plant with significant medicinal value. Its nuclear genome and chloroplast genome (plastome) have been reported, while there is a lack of genetic information on its mitogenome. We sequenced and assembled the complete mitogenome of R. idaeus, and conducted a series of genetic investigations comparing it with the nuclear and chloroplast genomes, so as to better gain a comprehensive understanding of the species' genetic background. RESULTS The mitogenome is represented by one circular chromosome of 438,947 bp. Twenty-four core genes, nine variable genes, 26 tRNAs, and three rRNAs were annotated. A total of 52 SSRs and 38 tandem repeat sequences were identified. 533 pairs of dispersed repeats were detected, among which three pairs were found to have mediated the homologous recombination, resulting in one major conformation and seven minor conformations. Furthermore, 52 homologous sequences between the mitogenome and plastome were identified, including six complete protein-coding genes and 12 tRNA genes. We also detected 828 homologous fragments between the nuclear genome and mitogenome, including one trnM-CAU gene. CONCLUSIONS In this study, we presented the mitogenome of R. idaeus for the first time based on data obtained from Illumina and Oxford Nanopore sequencing platforms. Key characteristics of the mitogenome were examined, including its gene composition, repetitive elements, and homologous DNA fragments. Additionally, we identified multiple recombination events in the mitogenome mediated by repetitive sequences The high-quality and well-annotated mitogenome for the known fruit red raspberry will provide essential genetic information for species classification, evolution analysis, and even genetic improvement in Rubus in the future.
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Affiliation(s)
- Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Minghui Yan
- Dabie Mountain Laboratory, College of Tea and Food Science, Xinyang Normal University, Xinyang, Henan, 464000, China
| | - Lijuan Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhuo Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ye Xiong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yusheng Wang
- School of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, 434025, China
| | - Caleb Onoja Akogwu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Olutayo Mary Tolulope
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Zhou
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Yanxia Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Zhang Y, Zhang J, Chen Z, Huang Y, Liu J, Liu Y, Yang Y, Jin X, Yang Y, Chen Y. Comparison of organelle genomes between endangered mangrove plant Dolichandrone spathacea to terrestrial relative provides insights into its origin and adaptative evolution. FRONTIERS IN PLANT SCIENCE 2024; 15:1442178. [PMID: 39376234 PMCID: PMC11457174 DOI: 10.3389/fpls.2024.1442178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 09/02/2024] [Indexed: 10/09/2024]
Abstract
Dolichandrone spathacea is a mangrove associate with high medicinal and ecological values. However, due to the dual-pressure of climate change and human activities, D. spathacea has become endangered in China. Moreover, misidentification between D. spathacea and its terrestrial relative D. cauda-felina poses further challenges to field protection and proper medicinal usage of D. spathacea. Thus, to address these problems, we sequenced and assembled mitochondrial (mt) and chloroplast (cp) genomes for both D. spathacea and D. cauda-felina. Comparative analysis revealed apparently different size and scaffold number between the two mt genomes, but a high similarity between the cp genomes. Eight regions with high sequence divergence were identified between the two cp genomes, which might be used for developing candidate DNA markers for distinguishing the two species. The splitting between D. spathacea and D. cauda-felina was inferred to occur at ~6.8 - 7.7 million years ago (Mya), which may be driven by the environment fluctuations in late Miocene. In the cp genome, 12 genes related to the expression of photosynthesis-associated proteins were detected with signatures of positive selection, which may contribute to the origin and evolutionary adaptation of Dolichandrone mangrove species. These new findings do not only enrich organelle genomic resources of Dolichandrone species, but also provide important genetic clues for improving the conservation and proper usage of endangered mangrove associate D. spathacea.
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Affiliation(s)
- Ying Zhang
- Hainan Academy of Forestry, Hainan Mangrove Research Institute, Haikou, China
- Mangrove Rare and Endangered Species Protection and Utilization Engineering Technology Research Center, Zhanjiang Key Laboratory of Mangrove Ecosystem Protection and Restoration, Lingnan Normal University, Zhanjiang, China
| | - Jingwen Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Zewei Chen
- Mangrove Rare and Endangered Species Protection and Utilization Engineering Technology Research Center, Zhanjiang Key Laboratory of Mangrove Ecosystem Protection and Restoration, Lingnan Normal University, Zhanjiang, China
| | - Yanni Huang
- Mangrove Rare and Endangered Species Protection and Utilization Engineering Technology Research Center, Zhanjiang Key Laboratory of Mangrove Ecosystem Protection and Restoration, Lingnan Normal University, Zhanjiang, China
| | - Jiaxuan Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yuqi Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yong Yang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Xiang Jin
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Yuchen Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yiqing Chen
- Hainan Academy of Forestry, Hainan Mangrove Research Institute, Haikou, China
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9
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Liu GH, Zuo YW, Shan Y, Yu J, Li JX, Chen Y, Gong XY, Liao XM. Structural analysis of the mitochondrial genome of Santalum album reveals a complex branched configuration. Genomics 2024; 116:110935. [PMID: 39243912 DOI: 10.1016/j.ygeno.2024.110935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/19/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
BACKGROUND Santalum album L. is an evergreen tree which is mainly distributes throughout tropical and temperate regions. And it has a great medicinal and economic value. RESULTS In this study, the complete mitochondrial genome of S. album were assembled and annotated, which could be descried by a complex branched structure consisting of three contigs. The lengths of these three contigs are 165,122 bp, 93,430 bp and 92,491 bp. We annotated 34 genes coding for proteins (PCGs), 26 tRNA genes, and 4 rRNA genes. The analysis of repeated elements shows that there are 89 SSRs and 242 pairs of dispersed repeats in S. album mitochondrial genome. Also we found 20 MTPTs among the chloroplast and mitochondria. The 20 MTPTs sequences span a combined length of 22,353 bp, making up 15.52 % of the plastome, 6.37 % of the mitochondrial genome. Additionally, by using the Deepred-mt tool, we found 628 RNA editing sites in 34 PCGs. Moreover, significant genomic rearrangement is observed between S. album and its associated mitochondrial genomes. Finally, based on mitochondrial genome PCGs, we deduced the phylogenetic ties between S. album and other angiosperms. CONCLUSIONS We reported the mitochondrial genome from Santalales for the first time, which provides a crucial genetic resource for our study of the evolution of mitochondrial genome.
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Affiliation(s)
- Guang-Hua Liu
- Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, Huaihua University, 418008 Huaihua, Hunan, China.; College of Biological and Food Engineering, Huaihua University, 418008 Huaihua, Hunan, China
| | - You-Wei Zuo
- Center for Biodiversity Conservation and Utilization, Key Laboratory of Eco-Environment in the Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, 400715 Beibei, Chongqing, China.
| | - Yuanyu Shan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China.
| | - Jia-Xi Li
- College of Biological and Food Engineering, Huaihua University, 418008 Huaihua, Hunan, China
| | - Ying Chen
- College of Biological and Food Engineering, Huaihua University, 418008 Huaihua, Hunan, China
| | - Xin-Yi Gong
- College of Biological and Food Engineering, Huaihua University, 418008 Huaihua, Hunan, China
| | - Xiao-Min Liao
- Hunan University of Medicine General Hospital, 418008 Huaihua, Hunan, China..
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10
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Luo X, Gu C, Gao S, Li M, Zhang H, Zhu S. Complete mitochondrial genome assembly of Zizania latifolia and comparative genome analysis. FRONTIERS IN PLANT SCIENCE 2024; 15:1381089. [PMID: 39184575 PMCID: PMC11341417 DOI: 10.3389/fpls.2024.1381089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 06/26/2024] [Indexed: 08/27/2024]
Abstract
Zizania latifolia (Griseb.) Turcz. ex Stapf has been cultivated as a popular aquatic vegetable in China due to its important nutritional, medicinal, ecological, and economic values. The complete mitochondrial genome (mitogenome) of Z. latifolia has not been previously studied and reported, which has hindered its molecular systematics and understanding of evolutionary processes. Here, we assembled the complete mitogenome of Z. latifolia and performed a comprehensive analysis including genome organization, repetitive sequences, RNA editing event, intercellular gene transfer, phylogenetic analysis, and comparative mitogenome analysis. The mitogenome of Z. latifolia was estimated to have a circular molecule of 392,219 bp and 58 genes consisting of three rRNA genes, 20 tRNA genes, and 35 protein-coding genes (PCGs). There were 46 and 20 simple sequence repeats (SSRs) with different motifs identified from the mitogenome and chloroplast genome of Z. latifolia, respectively. Furthermore, 49 homologous fragments were observed to transfer from the chloroplast genome to the mitogenome of Z. latifolia, accounting for 47,500 bp, presenting 12.1% of the whole mitogenome. In addition, there were 11 gene-containing homologous regions between the mitogenome and chloroplast genome of Z. latifolia. Also, approximately 85% of fragments from the mitogenome were duplicated in the Z. latifolia nuclear genome. Selection pressure analysis revealed that most of the mitochondrial genes were highly conserved except for ccmFc, ccmFn, matR, rps1, and rps3. A total of 93 RNA editing sites were found in the PCGs of the mitogenome. Z. latifolia and Oryza minuta are the most closely related, as shown by collinear analysis and the phylogenetic analysis. We found that repeat sequences and foreign sequences in the mitogenomes of Oryzoideae plants were associated with genome rearrangements. In general, the availability of the Z. latifolia mitogenome will contribute valuable information to our understanding of the molecular and genomic aspects of Zizania.
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Affiliation(s)
| | | | | | | | | | - Shidong Zhu
- College of Horticulture, Anhui Agricultural University, Hefei, China
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11
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Xie P, Wu J, Lu M, Tian T, Wang D, Luo Z, Yang D, Li L, Yang X, Liu D, Cheng H, Tan J, Yang H, Zhu D. Assembly and comparative analysis of the complete mitochondrial genome of Fritillaria ussuriensis Maxim. (Liliales: Liliaceae), an endangered medicinal plant. BMC Genomics 2024; 25:773. [PMID: 39118028 PMCID: PMC11312713 DOI: 10.1186/s12864-024-10680-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Fritillaria ussuriensis is an endangered medicinal plant known for its notable therapeutic properties. Unfortunately, its population has drastically declined due to the destruction of forest habitats. Thus, effectively protecting F. ussuriensis from extinction poses a significant challenge. A profound understanding of its genetic foundation is crucial. To date, research on the complete mitochondrial genome of F. ussuriensis has not yet been reported. RESULTS The complete mitochondrial genome of F. ussuriensis was sequenced and assembled by integrating PacBio and Illumina sequencing technologies, revealing 13 circular chromosomes totaling 737,569 bp with an average GC content of 45.41%. A total of 55 genes were annotated in this mitogenome, including 2 rRNA genes, 12 tRNA genes, and 41 PCGs. The mitochondrial genome of F. ussuriensis contained 192 SSRs and 4,027 dispersed repeats. In the PCGs of F. ussuriensis mitogenome, 90.00% of the RSCU values exceeding 1 exhibited a preference for A-ended or U-ended codons. In addition, 505 RNA editing sites were predicted across these PCGs. Selective pressure analysis suggested negative selection on most PCGs to preserve mitochondrial functionality, as the notable exception of the gene nad3 showed positive selection. Comparison between the mitochondrial and chloroplast genomes of F. ussuriensis revealed 20 homologous fragments totaling 8,954 bp. Nucleotide diversity analysis revealed the variation among genes, and gene atp9 was the most notable. Despite the conservation of GC content, mitogenome sizes varied significantly among six closely related species, and colinear analysis confirmed the lack of conservation in their genomic structures. Phylogenetic analysis indicated a close relationship between F. ussuriensis and Lilium tsingtauense. CONCLUSIONS In this study, we sequenced and annotated the mitogenome of F. ussuriensis and compared it with the mitogenomes of other closely related species. In addition to genomic features and evolutionary position, this study also provides valuable genomic resources to further understand and utilize this medicinal plant.
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Affiliation(s)
- Ping Xie
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Jingru Wu
- Affiliated Stomatological Hospital, Jiamusi University, Jiamusi, 154002, Heilongjiang, China
| | - Mengyue Lu
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Tongxin Tian
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Dongmei Wang
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Zhiwen Luo
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Donghong Yang
- Affiliated Stomatological Hospital, Jiamusi University, Jiamusi, 154002, Heilongjiang, China
| | - Lili Li
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Xuewen Yang
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Decai Liu
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Haitao Cheng
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Jiaxin Tan
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Hongsheng Yang
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China.
| | - Dequan Zhu
- School of Chinese Ethnic Medicine, Guizhou Minzu University, Guiyang, 550025, Guizhou, China.
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12
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Li L, Yang M, Qi Y, Yu Y, Gao P, Yang S, Zhao Y, Guo J, Liu J, Huang F, Yu L. Complete chloroplast genome and phylogenetic analysis of Amorphophallus paeoniifolius (Araceae). Mitochondrial DNA B Resour 2024; 9:865-870. [PMID: 39010881 PMCID: PMC11249165 DOI: 10.1080/23802359.2024.2378966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 07/07/2024] [Indexed: 07/17/2024] Open
Abstract
Amorphophallus paeoniifolius (Dennst.) Nicolson, 1885, often known as elephant foot yam, is a tropical tuber crop that originates from south-east Asia and belongs to the Araceae family. It is known for its high production potential and popularity as a medicinal plant. However, the phylogeny and genes for this species are still unavailable. In this study, the first complete chloroplast genome of A. paeoniifolius was reported and phylogenetic analysis was conducted with Araceae species. The chloroplast genome was 176,258 bp in length with 34.80% overall GC content and includes a large single-copy (LSC) region (93,951 bp), a small single-copy (SSC) region (15,013 bp), and a pair of inverted repeat (IRs) regions (33,647 bp). The chloroplast genome has 130 genes, which include 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. A maximum-likelihood (ML) phylogenetic analysis indicated that all Amorphophallus species formed a single monophyletic clade with a high bootstrap value and A. paeoniifolius was closely related to A. konjac, A. albus, A. krausei, and A. titanum. The chloroplast genome reported in this study will be useful for further taxonomic and evolutionary studies of Amorphophallus.
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Affiliation(s)
- Lifang Li
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Min Yang
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Ying Qi
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Yajun Yu
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Penghua Gao
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Shaowu Yang
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Yongteng Zhao
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Jianwei Guo
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Jiani Liu
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Feiyan Huang
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Lei Yu
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
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13
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Miao X, Yang W, Li D, Wang A, Li J, Deng X, He L, Niu J. Assembly and comparative analysis of the complete mitochondrial and chloroplast genome of Cyperus stoloniferus (Cyperaceae), a coastal plant possessing saline-alkali tolerance. BMC PLANT BIOLOGY 2024; 24:628. [PMID: 38961375 PMCID: PMC11220973 DOI: 10.1186/s12870-024-05333-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
BACKGROUND Cyperus stoloniferus is an important species in coastal ecosystems and possesses economic and ecological value. To elucidate the structural characteristics, variation, and evolution of the organelle genome of C. stoloniferus, we sequenced, assembled, and compared its mitochondrial and chloroplast genomes. RESULTS We assembled the mitochondrial and chloroplast genomes of C. stoloniferus. The total length of the mitochondrial genome (mtDNA) was 927,413 bp, with a GC content of 40.59%. It consists of two circular DNAs, including 37 protein-coding genes (PCGs), 22 tRNAs, and five rRNAs. The length of the chloroplast genome (cpDNA) was 186,204 bp, containing 93 PCGs, 40 tRNAs, and 8 rRNAs. The mtDNA and cpDNA contained 81 and 129 tandem repeats, respectively, and 346 and 1,170 dispersed repeats, respectively, both of which have 270 simple sequence repeats. The third high-frequency codon (RSCU > 1) in the organellar genome tended to end at A or U, whereas the low-frequency codon (RSCU < 1) tended to end at G or C. The RNA editing sites of the PCGs were relatively few, with only 9 and 23 sites in the mtDNA and cpDNA, respectively. A total of 28 mitochondrial plastid DNAs (MTPTs) in the mtDNA were derived from cpDNA, including three complete trnT-GGU, trnH-GUG, and trnS-GCU. Phylogeny and collinearity indicated that the relationship between C. stoloniferus and C. rotundus are closest. The mitochondrial rns gene exhibited the greatest nucleotide variability, whereas the chloroplast gene with the greatest nucleotide variability was infA. Most PCGs in the organellar genome are negatively selected and highly evolutionarily conserved. Only six mitochondrial genes and two chloroplast genes exhibited Ka/Ks > 1; in particular, atp9, atp6, and rps7 may have undergone potential positive selection. CONCLUSION We assembled and validated the mtDNA of C. stoloniferus, which contains a 15,034 bp reverse complementary sequence. The organelle genome sequence of C. stoloniferus provides valuable genomic resources for species identification, evolution, and comparative genomic research in Cyperaceae.
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Affiliation(s)
- Xiaorong Miao
- College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Wenwen Yang
- College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Donghai Li
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, 537000, China
| | - Aiqin Wang
- College of Agriculture, Guangxi University, Nanning, 530004, China.
| | - Juanyun Li
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, 537000, China
| | - Xu Deng
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, 537000, China
| | - Longfei He
- College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Junqi Niu
- College of Agriculture, Guangxi University, Nanning, 530004, China.
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, 537000, China.
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14
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Hao Z, Jiang X, Pan L, Guo J, Chen Y, Li J, Liu B, Guo A, Luo L, Jia R. The complete mitochondrial genome of Pontederia crassipes: using HiFi reads to investigate genome recombination and gene transfer from chloroplast genome. FRONTIERS IN PLANT SCIENCE 2024; 15:1407309. [PMID: 39006960 PMCID: PMC11240117 DOI: 10.3389/fpls.2024.1407309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/12/2024] [Indexed: 07/16/2024]
Abstract
Water hyacinth (Pontederia crassipes Mart.) is a monocotyledonous aquatic plant renowned for its rapid growth, extensive proliferation, biological invasiveness, and ecological resilience to variations in pH, nutrients, and temperature. The International Union for Conservation of Nature (IUCN) has listed P. crassipes among the top 100 invasive species. However, comprehensive genomic information, particularly concerning its mitochondrial genome (mitogenome), remains surprisingly limited. In this study, the complete mitogenome of P. crassipes was analyzed using bioinformatics approaches. The mitogenome is 399,263 bp long and contains 38 protein-coding genes (PCGs), 24 tRNA genes, and 3 rRNA genes. Sequence analysis revealed that the complete mitogenome of the species contains 3,289 dispersed repeats, and 765 RNA editing sites in protein-coding genes. The P. crassipes mitogenome possessed un-conserved structures, including extensive sequence transfer between its chloroplasts and mitochondria. Our study on the mitogenome of P. crassipes offers critical insights into its evolutionary patterns and phylogenetic relationships with related taxa. This research enhances our understanding of this invasive species, known for its significant biomass and rapid overgrowth in aquatic environments.
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Affiliation(s)
- Zhigang Hao
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
- Hainan Seed Industry Laboratory, Sanya, Hainan, China
- Department of Plant Pathology, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Xiaoqi Jiang
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Lei Pan
- CAIQ Center for Biosafety in Sanya, Sanya, Hainan, China
| | - Jingyuan Guo
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Yi Chen
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Jianqiang Li
- Department of Plant Pathology, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Biao Liu
- Ministry of Ecology and Environment, Nanjing Institute of Environmental Sciences, Nanjing, China
| | - Anping Guo
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Laixin Luo
- Department of Plant Pathology, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Ruizong Jia
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
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15
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Tong W, Yu D, Zhu X, Le Z, Chen H, Hu F, Wu S. The Whole Mitochondrial Genome Sequence of Dendrobium loddigesii Rolfe, an Endangered Orchid Species in China, Reveals a Complex Multi-Chromosome Structure. Genes (Basel) 2024; 15:834. [PMID: 39062613 PMCID: PMC11275824 DOI: 10.3390/genes15070834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/28/2024] Open
Abstract
Dendrobium loddigesii is a precious traditional Chinese medicine with high medicinal and ornamental value. However, the characterization of its mitochondrial genome is still pending. Here, we assembled the complete mitochondrial genome of D. loddigesii and discovered that its genome possessed a complex multi-chromosome structure. The mitogenome of D. loddigesii consisted of 17 circular subgenomes, ranging in size from 16,323 bp to 56,781 bp. The total length of the mitogenome was 513,356 bp, with a GC content of 43.41%. The mitogenome contained 70 genes, comprising 36 protein-coding genes (PCGs), 31 tRNA genes, and 3 rRNA genes. Furthermore, we detected 403 repeat sequences as well as identified 482 RNA-editing sites and 8154 codons across all PCGs. Following the sequence similarity analysis, 27 fragments exhibiting homology to both the mitogenome and chloroplast genome were discovered, accounting for 9.86% mitogenome of D. loddigesii. Synteny analysis revealed numerous sequence rearrangements in D. loddigesii and the mitogenomes of related species. Phylogenetic analysis strongly supported that D. loddigesii and D. Amplum formed a single clade with 100% bootstrap support. The outcomes will significantly augment the orchid mitochondrial genome database, offering profound insights into Dendrobium's intricate mitochondrial genome architecture.
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Affiliation(s)
| | | | | | | | | | | | - Shengmin Wu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China; (W.T.); (D.Y.); (X.Z.); (Z.L.); (H.C.); (F.H.)
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16
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Xie Y, Liu W, Guo L, Zhang X. Mitochondrial genome complexity in Stemona sessilifolia: nanopore sequencing reveals chloroplast gene transfer and DNA rearrangements. Front Genet 2024; 15:1395805. [PMID: 38903753 PMCID: PMC11188483 DOI: 10.3389/fgene.2024.1395805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/17/2024] [Indexed: 06/22/2024] Open
Abstract
Mitochondria are semi-autonomous organelles in eukaryotic cells with their own genome. Plant mitogenomes differ from animal mitogenomes in size, structure, and repetitive DNA sequences. Despite larger sizes, plant mitogenomes do not have significantly more genes. They exhibit diverse structures due to variations in size, repetitive DNA, recombination frequencies, low gene densities, and reduced nucleotide substitution rates. In this study, we analyzed the mitochondrial genome of Stemona sessilifolia using Nanopore and Illumina sequencing. De-novo assembly and annotation were conducted using Unicycler, Geseq, tRNAscan-SE and BLASTN, followed by codon usage, repeat sequence, RNA-editing, synteny, and phylogenetic analyses. S. sessilifolia's mitogenome consisted of one linear contig and six circular contigs totaling 724,751 bp. It had 39 protein-coding genes, 27 tRNA genes, and 3 rRNA genes. Transfer of chloroplast sequences accounted for 13.14% of the mitogenome. Various analyses provided insights into genetic characteristics, evolutionary dynamics, and phylogenetic placement. Further investigations can explore transferred genes' functions and RNA-editing's role in mitochondrial gene expression in S. sessilifolia.
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Affiliation(s)
- Yuning Xie
- School of Public Health, North China University of Science and Technology, Tangshan, China
| | - Wenqiong Liu
- Public Health Department, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Liwen Guo
- College of Life Science, North China University of Science and Technology, Tangshan, China
| | - Xuemei Zhang
- School of Public Health, North China University of Science and Technology, Tangshan, China
- College of Life Science, North China University of Science and Technology, Tangshan, China
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17
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Shan Y, Li J, Duan X, Zhang X, Yu J. Elucidating the multichromosomal structure within the Brasenia schreberi mitochondrial genome through assembly and analysis. BMC Genomics 2024; 25:422. [PMID: 38684976 PMCID: PMC11059650 DOI: 10.1186/s12864-024-10331-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
Brasenia schreberi, a plant species traditionally utilized in Chinese medicine and cuisine, represents an early evolutionary stage among flowering plants (angiosperms). While the plastid genome of this species has been published, its mitochondrial genome (mitogenome) has not been extensively explored, with a notable absence of thorough comparative analyses of its organellar genomes. In our study, we had assembled the entire mitogenome of B. schreberi utilizing the sequencing data derived from both Illumina platform and Oxford Nanopore. The B. schreberi mitogenome mostly exists as six circular DNA molecules, with the largest being 628,257 base pairs (bp) and the smallest 110,220 bp, amounting to 1.49 megabases (Mb). Then we annotated the mitogenome of B. schreberi. The mitogenome encompasses a total of 71 genes: 40 of these are coding proteins genes (PCGs), 28 are genes for transfer RNA (tRNA), and the remaining 3 are genes for ribosomal RNA (rRNA). In the analysis of codon usage, we noted a unique codon preference specific to each amino acid. The most commonly used codons exhibited an average RSCU of 1.36, indicating a noticeable bias in codon selection. In the repeat sequence analysis, a total of 553 simple sequence repeats (SSRs) were identified, 1,822 dispersed repeats (comprising 1,015 forward and 807 palindromic repeats), and 608 long terminal repeats (LTRs). Additionally, in the analysis of homologous sequences between organelle genomes, we detected 38 homologous sequences derived from the plastid genome, each exceeding 500 bp, within the B. schreberi mitochondrial genome. Notably, ten tRNA genes (trnC-GCA, trnM-CAU, trnI-CAU, trnQ-UUG, trnN-GUU, trnT-GGU, trnW-CCA, trnA-UGC, trnI-GAU, and trnV-GAC) appear to have been completely transferred from the chloroplast to the mitogenome. Utilizing the Deepred-mt to predict the RNA editing sites in the mitogenome, we have identified 675 high-quality RNA editing sites in the 40 mitochondrial PCGs. In the final stage of our study, we performed an analysis of colinearity and inferred the phylogenetic relationship of B. schreberi with other angiosperms, utilizing the mitochondrial PCGs as a basis. The results showed that the non-coding regions of the B. schreberi mitogenome are characterized by an abundance of repetitive sequences and exogenous sequences, and B. schreberi is more closely related with Euryale ferox.
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Affiliation(s)
- Yuanyu Shan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Xinmei Duan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Xue Zhang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China.
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing, 400715, China.
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18
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Gao Y, Yin S. The complete chloroplast genome assembly of Amorphophallus kiusianus makino 1913 (araceae) from Southern China. Mitochondrial DNA B Resour 2024; 9:522-526. [PMID: 38634040 PMCID: PMC11022911 DOI: 10.1080/23802359.2024.2342934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
The mountainous region of southern China has been characterized by its complicated environment and topography. Amorphophallus kiusianus Makino 1913 is a representative species of extreme habitat preference that resides mainly in this region. To help study the genetic differentiation mechanisms of A. kiusianus populations, we sequenced the first chloroplast genome of this species using next-generation sequencing. The chloroplast genome was 166,269 bp in length with an average GC content of 36% (GenBank accession number: PP072243). The lengths of the large single-copy region (LSC), small single-copy region (SSC), and two inverted repeats (IRs) were 90,701 bp, 14,802 bp, 31,383 bp, and 31,383 bp, respectively. One hundred and twenty-nine genes were annotated in the chloroplast genome, including 84 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The phylogenetic tree suggested a close relationship among A. kiusianus, A. yunnanensis, and A. coaetaneus. The chloroplast genome reported in this study provides valuable genomic resources for the future phylogeographic research of A. kiusianus.
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Affiliation(s)
- Yong Gao
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan, China
| | - Si Yin
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan, China
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Gao Y, Yin S. Assembly and analysis of the chloroplast genome of Amorphophallus kachinensis Engler & Gehrmann (Araceae) from Southwestern China: implications for conservation and utilization. Mitochondrial DNA B Resour 2024; 9:452-456. [PMID: 38586510 PMCID: PMC10993747 DOI: 10.1080/23802359.2024.2338550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/31/2024] [Indexed: 04/09/2024] Open
Abstract
Konjac glucomannan consists of D-mannose and D-glucose units and is a hydrocolloid obtained from the corm of Amorphophallus species. Due to its bioactive properties, biodegradability, and hydrophilic ability, glucomannan is widely used in the fields of food, medicine, and industry. Amorphophallus species have been cultivated as cash crops in many Asian countries. Amorphophallus kachinensis Engler & Gehrmann 1911 is naturally distributed in southwestern China, Laos, and northern Thailand. To help the genetic assessment and conservation of this species, the first chloroplast genome of A. kachinensis was sequenced on the Illumina sequencing platform. We assembled the chloroplast genome using the software GetOrganelle and annotated the genome by Geseq and Cpgavas 2. The assembled chloroplast genome was 173,330 bp long, and the average GC content was 35% (GenBank accession number: PP072244). The chloroplast genome of A. kachinensis contained one large single copy, one small single copy, and two inverted repeats, with lengths of 92,030 bp, 15,118 bp, 33,091 bp, and 33,091 bp, respectively. We successfully annotated 132 genes across the genome, which was consistent with other Amorphophallus species. The phylogenetic tree indicates a sub-divergence in the Amorphophallus genus with two main genetic groups detected among eight species. The two genetic groups should be treated as distinct evolutionarily significant units when making conservation strategies. Our study enriched the chloroplast genome resources of the Amorphophallus genus and could help future phylogeographic studies, protection, and utilization of wild resources.
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Affiliation(s)
- Yong Gao
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
| | - Si Yin
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
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Hao Z, Zhang Z, Zhang J, Cui X, Li J, Luo L, Li Y. The complete mitochondrial genome of Aglaia odorata, insights into its genomic structure and RNA editing sites. FRONTIERS IN PLANT SCIENCE 2024; 15:1362045. [PMID: 38510436 PMCID: PMC10950942 DOI: 10.3389/fpls.2024.1362045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/21/2024] [Indexed: 03/22/2024]
Abstract
Aglaia odorata, native to Guangdong, Guangxi, and Hainan provinces in China, has long been utilized as an herbal remedy in ancient China. In this study, we assembled and annotated the complete mitochondrial genome (mitogenome) of A. odorata, which spans a total length of 537,321 bp. Conformation of the A. odorata recombination was verified through PCR experiments and Sanger sequencing. We identified and annotated 35 protein-coding genes (PCGs), 22 tRNA genes, and 3 rRNA genes within the mitogenome. Analysis of repeated elements revealed the presence of 192 SSRs, 29 pairs of tandem repeats, and 333 pairs of dispersed repeats in the A. odorata mitogenome. Additionally, we analyzed codon usage and mitochondrial plastid DNAs (MTPTs). Twelve MTPTs between the plastome and mitogenome of A. odorata were identified, with a combined length of 2,501 bp, accounting for 0.47% of the mitogenome. Furthermore, 359 high-confidence C to U RNA editing sites were predicted on PCGs, and four selected RNA editing sites were specially examined to verify the creation of start and/or stop codons. Extensive genomic rearrangement was observed between A. odorata and related mitogenomes. Phylogenetic analysis based on mitochondrial PCGs were conducted to elucidate the evolutionary relationships between A. odorata and other angiosperms.
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Affiliation(s)
- Zhigang Hao
- Department of Pesticide Science, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China
- Sanya Institute of China Agricultural University, Sanya, Hainan, China
- Hainan Seed Industry Laboratory, Sanya, Hainan, China
| | - Zhiping Zhang
- Department of Pesticide Science, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Jinan Zhang
- Sanya Institute of China Agricultural University, Sanya, Hainan, China
| | - Xiufen Cui
- Hainan Seed Industry Laboratory, Sanya, Hainan, China
- Department of Plant Pathology, Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, China
| | - Jianqiang Li
- Hainan Seed Industry Laboratory, Sanya, Hainan, China
- Department of Plant Pathology, Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, China
| | - Laixin Luo
- Hainan Seed Industry Laboratory, Sanya, Hainan, China
- MOA Key Lab of Pest Monitoring and Green Management, China Agricultural University, Beijing, China
| | - Yingbin Li
- Department of Pesticide Science, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China
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Li C, Liu H, Qin M, Tan YJ, Ou XL, Chen XY, Wei Y, Zhang ZJ, Lei M. RNA editing events and expression profiles of mitochondrial protein-coding genes in the endemic and endangered medicinal plant, Corydalis saxicola. FRONTIERS IN PLANT SCIENCE 2024; 15:1332460. [PMID: 38379941 PMCID: PMC10876856 DOI: 10.3389/fpls.2024.1332460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024]
Abstract
Corydalis saxicola, an endangered medicinal plant endemic to karst habitats, is widely used in Traditional Chinese Medicine to treat hepatitis, abdominal pain, bleeding hemorrhoids and other conditions. However, to date, the mitochondrial (mt) genome of C. saxicola has not been reported, which limits our understanding of the genetic and biological mechanisms of C. saxicola. Here, the mt genome of C. saxicola was assembled by combining the Nanopore and Illumina reads. The mt genome of C. saxicola is represented by a circular chromosome which is 587,939 bp in length, with an overall GC content of 46.50%. 40 unique protein-coding genes (PCGs), 22 tRNA genes and three rRNA genes were identified. Codon usage of the PCGs was investigated and 167 simple sequence repeats were identified. Twelve homologous fragments were identified between the mt and ct genomes of C. saxicola, accounting for 1.04% of the entire mt genome. Phylogenetic examination of the mt genomes of C. saxicola and 30 other taxa provided an understanding of their evolutionary relationships. We also predicted 779 RNA editing sites in 40 C. saxicola mt PCGs and successfully validated 506 (65%) of these using PCR amplification and Sanger sequencing. In addition, we transcriptionally profiled 24 core mt PCGs in C. saxicola roots treated with different concentrations of CaCl2, as well as in other organs. These investigations will be useful for effective utilization and molecular breeding, and will also provide a reference for further studies of the genus Corydalis.
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Affiliation(s)
- Cui Li
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Han Liu
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Mei Qin
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Yao-jing Tan
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Xia-lian Ou
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Xiao-ying Chen
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ying Wei
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Zhan-jiang Zhang
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ming Lei
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
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Han Y, Feng YL, Wang J, Zhu SS, Jin XJ, Wu ZQ, Zhang YH. Comprehensive Analysis of the Complete Mitochondrial Genome of Rehmannia chingii: An Autotrophic Species in the Orobanchaceae Family. Genes (Basel) 2024; 15:98. [PMID: 38254987 PMCID: PMC10815111 DOI: 10.3390/genes15010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Rehmannia chingii is an important medicinal plant with immense value in scientific research. However, its mitochondrial genome (mitogenome) has not yet been characterized. Herein, based on whole-genome Illumina short reads and PacBio HiFi reads, we obtained the complete mitogenome of R. chingii through a de novo assembly strategy. We carried out comparative genomic analyses and found that, in comparison with the plastid genome (plastome) showing a high degree of structural conservation, the R. chingii mitogenome structure is relatively complex, showing an intricate ring structure with 16 connections, owing to five repetitive sequences. The R. chingii mitogenome was 783,161 bp with a GC content of 44.8% and contained 77 genes, comprising 47 protein-coding genes (CDS), 27 tRNA genes, and 3 rRNA genes. We counted 579 RNA editing events in 47 CDS and 12,828 codons in all CDSs of the R. chingii mitogenome. Furthermore, 24 unique sequence transfer fragments were found between the mitogenome and plastome, comprising 8 mitogenome CDS genes and 16 plastome CDS genes, corresponding to 2.39% of the R. chingii mitogenome. Mitogenomes had shorter but more collinear regions, evidenced by a comparison of the organelles of non-parasitic R. chingii, hemiparasitic Pedicularis chinensis, and holoparasitic Aeginetia indica in the Orobanchaceae family. Moreover, from non-parasitic to holoparasitic species, the genome size in the mitogenomes of Orobanchaceae species did not decrease gradually. Instead, the smallest mitogenome was found in the hemiparasitic species P. chinensis, with a size of 225,612 bp. The findings fill the gap in the mitogenome research of the medicinal plant R. chingii, promote the progress of the organelle genome research of the Orobanchaceae family, and provide clues for molecular breeding.
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Affiliation(s)
- Ying Han
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Y.H.); (X.-J.J.)
| | - Yan-Lei Feng
- College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China;
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China;
| | - Shan-Shan Zhu
- School of Marine Sciences, Ningbo University, Ningbo 315211, China;
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
| | - Xin-Jie Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Y.H.); (X.-J.J.)
- Institute for Eco-Environmental Research of Sanyang Wetland, Wenzhou University, Wenzhou 325035, China
| | - Zhi-Qiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China;
| | - Yong-Hua Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Y.H.); (X.-J.J.)
- Institute for Eco-Environmental Research of Sanyang Wetland, Wenzhou University, Wenzhou 325035, China
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Yin S, Gao Y. Characterization of the complete chloroplast genome assembly of Amorphophallus yunnanensis Engler, Pflanzenr (Araceae) from southwestern China. Mitochondrial DNA B Resour 2023; 8:1445-1449. [PMID: 38173919 PMCID: PMC10763844 DOI: 10.1080/23802359.2023.2294896] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/09/2023] [Indexed: 01/05/2024] Open
Abstract
Southwestern China is a biodiversity hotspot due to its diverse topography and environment. Amorphophallus yunnanensis is a species of perennial herb that is mainly distributed throughout southwestern China. The genetic diversity and divergence in this species have not been assessed largely due to a lack of genomic resources. To help with the phylogeographic study, we sequenced and assembled the first complete chloroplast genome sequence of A. yunnanensis. The length of the chloroplast genome was 164,417 bp, with an average GC content of 36% (GenBank accession no. OR400247). The genome possessed a typical quadripartite structure, and the lengths of the large single-copy (LSC), small single-copy (SSC), and two inverted repeat (IR) regions were 92,149 bp, 15,182 bp, 28,543bp, and 28,543bp, respectively. A total of 128 genes were annotated across the genome, including 82 protein-coding genes, 8 rRNAs, and 38 tRNAs. The maximum likelihood (ML) phylogeny confirmed the phylogenetic position of Amorphophallus within Araceae, with the Amorphophallus species forming a single monophyletic clade with a high bootstrap value. The ML tree also indicated that A. yunnanensis was most closely related to A. coaetaneus. This newly sequenced chloroplast genome assembly will aid in future studies of genetic diversity, historical population dynamics, and geographic differentiation patterns of A. yunnanensis.
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Affiliation(s)
- Si Yin
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan, China
| | - Yong Gao
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan, China
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Liu Q, Wu Z, Tian C, Yang Y, Liu L, Feng Y, Li Z. Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1266797. [PMID: 38155854 PMCID: PMC10753190 DOI: 10.3389/fpls.2023.1266797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
Introduction Prunus pedunculata (Prunoideae: Rosaceae), a relic shrub with strong resistance and multiple application values, is endangered in China. Extensive research had been devoted to gene expression, molecular markers, plastid genome analysis, and genetic background investigations of P. pedunculata. However, the mitochondrial genome of this species has not been systematically described, owing to the complexity of the plant mitogenome. Methods In the present research, the complete mitochondrial genome of P. pedunculata was assembled, annotated, and characterized. The genomic features, gene content and repetitive sequences were analyzed. The genomic variation and phylogenetic analysis have been extensively enumerated. Results and discussion The P. pedunculata mitogenome is a circular molecule with a total length of 405,855 bp and a GC content of 45.63%, which are the smallest size and highest GC content among the known Prunus mitochondrial genomes. The mitogenome of P. pedunculata encodes 62 genes, including 34 unique protein-coding genes (PCGs, excluding three possible pseudogenes), three ribosomal RNA genes, and 19 transfer RNA genes. The mitogenome is rich in repetitive sequences, counting 112 simple sequence repeats, 15 tandem repeats, and 50 interspersed repetitive sequences, with a total repeat length of 11,793 bp, accounting for 2.91% of the complete genome. Leucine (Leu) was a predominant amino acid in PCGs, with a frequency of 10.67%, whereas cysteine (Cys) and tryptophan (Trp) were the least adopted. The most frequently used codon was UUU (Phe), with a relative synonymous codon usage (RSCU) value of 1.12. Selective pressure was calculated based on 20 shared PCGs in the mitogenomes of the 32 species, most of which were subjected to purifying selection (Ka/Ks < 1), whereas ccmC and ccmFn underwent positive selection. A total of 262 potential RNA editing sites in 26 PCGs were identified. Furthermore, 56 chloroplast-derived fragments were ascertained in the mitogenome, ranging from 30 to 858 bp, and were mainly located across IGS (intergenic spacer) regions or rRNA genes. These findings verify the occurrence of intracellular gene transfer events from the chloroplast to the mitochondria. Furthermore, the phylogenetic relationship of P. pedunculata was supported by the mitogenome data of 30 other taxa of the Rosaceae family. Understanding the mitochondrial genome characteristics of P. pedunculata is of great importance to promote comprehension of its genetic background and this study provides a basis for the genetic breeding of Prunus.
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Affiliation(s)
- Qian Liu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Zinian Wu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China
| | - Chunyu Tian
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Yanting Yang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Lemeng Liu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Yumei Feng
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Zhiyong Li
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China
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Yin S, Gao Y. The complete chloroplast genome assembly of Amorphophallus krausei Engler, Pflanzenr 1911 (Araceae) from southwestern China. Mitochondrial DNA B Resour 2023; 8:1339-1342. [PMID: 38196792 PMCID: PMC10776054 DOI: 10.1080/23802359.2023.2288889] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/24/2023] [Indexed: 01/11/2024] Open
Abstract
Plants in the genus Amorphophallus, many of which possess high konjac glucomannan content, are considered important cash crops in many Asian countries. Wild relatives of cultivated Amorphophallus species are valuable resources for the genetic improvement of these crops. To aid in future genetic research of wild germplasm resources of Amorphophallus, a single individual of Amorphophallus krausei Engler, Pflanzenr 1911 was collected from southwestern China, and its chloroplast genome was sequenced using next-generation sequencing technologies. The assembled chloroplast genome was 172,418 bp in length with a GC content of 35.23% (GenBank accession no. OR416863). A typical quadripartite structure was found in the genome, which was comprised of one large single-copy (LSC), one small single-copy (SSC), and two inverted repeats (IRs), with lengths of 91,983 bp, 15,591 bp, 32,422 bp, and 32,422 bp, respectively. A total of 132 genes were annotated in the genome, including 86 protein-coding genes, 38 tRNAs, and 8 rRNAs. A maximum likelihood (ML) tree of A. krausei and 17 other species in the family Araceae suggested that all Amorphophallus species formed a single monophyletic clade. A close relationship among A. konjac, A. albus, and A. krausei was also revealed by the phylogenetic tree. The newly sequenced chloroplast genome of A. krausei will support future genetic studies, particularly the assessment of genetic diversity, resource conservation, and phylogeographic research.
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Affiliation(s)
- Si Yin
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan, China
| | - Yong Gao
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan, China
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